NM_013450.4:c.1294-1203G>A

Variant names:

• chr2-159434566-C-T
• rs740
• NM_013450.4:c.1294-1203G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_013450.4(BAZ2B):​c.1294-1203G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.324 in 151,874 control chromosomes in the GnomAD database, including 9,800 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.32 (9799 hom., cov: 32)
  • Exomes 𝑓: 0.50 (1 hom.)
• Consequence: BAZ2B NM_013450.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.317
• Publications: 6 publications found

Genes affected

BAZ2B (HGNC:963): (bromodomain adjacent to zinc finger domain 2B) This gene belongs to the bromodomain gene family. Members of this gene family encode proteins that are integral components of chromatin remodeling complexes. The encoded protein showed strong preference for the activating H3K14Ac mark in a histone peptide screen, suggesting a potential role in transcriptional activation. This gene may be associated with susceptibility to sudden cardiac death (SCD). [provided by RefSeq, Aug 2016]

BAZ2B Gene-Disease associations (from GenCC):

• neurodevelopmental disorder

  Inheritance: AD Classification: STRONG, LIMITED Submitted by: G2P, Ambry Genetics
• complex neurodevelopmental disorder

  Inheritance: AD Classification: LIMITED Submitted by: ClinGen

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.452 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_013450.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BAZ2B	NM_013450.4	MANE Select	c.1294-1203G>A		intron	N/A	NP_038478.2
	BAZ2B	NM_001329857.2		c.1105-1203G>A		intron	N/A	NP_001316786.1
	BAZ2B	NM_001329858.2		c.1294-1203G>A		intron	N/A	NP_001316787.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BAZ2B	ENST00000392783.7	TSL:5 MANE Select	c.1294-1203G>A		intron	N/A	ENSP00000376534.2
	BAZ2B	ENST00000392782.5	TSL:1	c.1288-1203G>A		intron	N/A	ENSP00000376533.1
	BAZ2B	ENST00000472953.1	TSL:5	n.988G>A		non_coding_transcript_exon	Exon 1 of 8

Frequencies

GnomAD3 genomes AF: 0.324 AC: 49210 AN: 151748 Hom.: 9795 Cov.: 32

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.639

Gnomad AMR AF: 0.297

Gnomad ASJ AF: 0.330

Gnomad EAS AF: 0.286

Gnomad SAS AF: 0.190

Gnomad FIN AF: 0.338

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.456

Gnomad OTH AF: 0.344

GnomAD4 exome AF: 0.500 AC: 4 AN: 8 Hom.: 1 Cov.: 0 AF XY: 0.250 AC XY: 1 AN XY: 4

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AF: 0.500 AC: 1 AN: 2

European-Non Finnish (NFE) AF: 0.500 AC: 3 AN: 6

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.324 AC: 49232 AN: 151866 Hom.: 9799 Cov.: 32 AF XY: 0.314 AC XY: 23290 AN XY: 74232

African (AFR) AF: 0.127 AC: 5278 AN: 41514

American (AMR) AF: 0.296 AC: 4515 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.330 AC: 1145 AN: 3472

East Asian (EAS) AF: 0.286 AC: 1480 AN: 5170

South Asian (SAS) AF: 0.191 AC: 918 AN: 4814

European-Finnish (FIN) AF: 0.338 AC: 3566 AN: 10542

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.456 AC: 30906 AN: 67806

Other (OTH) AF: 0.345 AC: 728 AN: 2110

Alfa AF: 0.374 Hom.: 1607

Bravo AF: 0.316

Asia WGS AF: 0.240 AC: 838 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	3.4
DANN	Benign	0.70
PhyloP100		0.32
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs740; hg19: chr2-160291077;